rs2148575

Positions:

• chr5-34258360-A-G
• chr5-34258360-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000658746.1(ENSG00000286543):​n.135+12953A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 151,654 control chromosomes in the GnomAD database, including 54,605 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.82 (54605 hom., cov: 29)
• Consequence: ENST00000658746.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000658746.1	n.135+12953A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124341 AN: 151536 Hom.: 54597 Cov.: 29

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.906

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.945

Gnomad FIN AF: 0.902

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.972

Gnomad OTH AF: 0.862

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.820 AC: 124381 AN: 151654 Hom.: 54605 Cov.: 29 AF XY: 0.822 AC XY: 60908 AN XY: 74088

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.931

Gnomad4 ASJ AF: 0.967

Gnomad4 EAS AF: 0.887

Gnomad4 SAS AF: 0.945

Gnomad4 FIN AF: 0.902

Gnomad4 NFE AF: 0.972

Gnomad4 OTH AF: 0.863

Alfa AF: 0.927 Hom.: 23424

Bravo AF: 0.805

Asia WGS AF: 0.902 AC: 3123 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	2.1
DANN	Benign	0.51

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2148575; hg19: chr5-34258465;